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Commentary

Scientific American assesses naturalistic explanations for the origin of life

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From Scientific American. (H/T Letitia via Mary)

Excerpt:

As recently as the middle of the 20th century, many scientists thought that the first organisms were made of self-replicating proteins. After Francis Crick and James Watson showed that DNA is the basis for genetic transmission in the 1950s, many researchers began to favor nucleic acids over proteins as the ur-molecules. But there was a major hitch in this scenario. DNA can make neither proteins nor copies of itself without the help of catalytic proteins called enzymes. This fact turned the origin of life into a classic chicken-or-egg puzzle: Which came first, proteins or DNA?

RNA, DNA’s helpmate, remains the most popular answer to this conundrum, just as it was when I wrote “In the Beginning…” Certain forms of RNA can act as their own enzymes, snipping themselves in two and splicing themselves back together again. If RNA could act as an enzyme, then it might be able to replicate itself without help from proteins. RNA could serve as gene and catalyst, egg and chicken.

But the “RNA-world” hypothesis remains problematic. RNA and its components are difficult to synthesize under the best of circumstances, in a laboratory, let alone under plausible prebiotic conditions. Once RNA is synthesized, it can make new copies of itself only with a great deal of chemical coaxing from the scientist. Overbye notes that “even if RNA did appear naturally, the odds that it would happen in the right sequence to drive Darwinian evolution seem small.”

The RNA world is so dissatisfying that some frustrated scientists are resorting to much more far out—literally—speculation. The most startling revelation in Overbye’s article is that scientists have resuscitated a proposal once floated by Crick. Dissatisfied with conventional theories of life’s beginning, Crick conjectured that aliens came to Earth in a spaceship and planted the seeds of life here billions of years ago. This notion is called directed panspermia. In less dramatic versions of panspermia, microbes arrived on our planet via asteroids, comets or meteorites, or drifted down like confetti.

John Horgan is not a Christian, nor even a theist. This is the state of the art if you are a naturalist.

Basically, you have at most a couple hundred million years from the time the Earth cools to the appearance of first life. You are unlikely to get one measly protein without an intelligence arranging the amino acids. This is assuming we spot you a favorable environment for creating amino acids without intervention. And then there would still be the problem of sequencing the proteins.

Atheists oppose science and evidence

Theists support science and evidence

News

Should ID researchers be “marked down” for defending intelligent design?

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Here’s an interesting post from Evolution News about a teacher in New Zealand who grades her students down if they try to discuss intelligent design in class.

Excerpt:

Biology lecturer Alison Campbell at the University of Waikato in Hillcrest, New Zealand, exemplifies a mindset that is tragically common in academia. She openly boasts that if a student were to use standard ID arguments such as the irreducible complexity of the bacterial flagellum, that student would be “marked down”:

If, for example, a student were to use examples such as the bacterial flagellum to advance an ID view then they should expect to be marked down; that particular creationist trophe has been well & truly discredited.

And in fact in reading over that post by Alison Campbell and the comments, it’s not clear that she has read anything by an ID theorist. She quotes from a an anti-ID philosopher and a anti-ID judge to argue against intelligent design. She doesn’t interact with any intelligent design books, by quoting pro-ID  arguments and citing page numbers. She doesn’t mention a single research paper written by an ID theorist. It’s just something that an English teacher could have written. She has to keep everything very vague in that post. “There is lots of evidence against ID, so let me quote a philosopher”. “There is lots of evidence against ID, so let me quote a judge”. Neither of those authorities has any training in biology. Does Alison Campbell? Let’s see.

Here are some of her recent publications:

Campbell, A. 2009 You let them talk in lectures? Student discussion as formative assessment . In: Meyer, Luanna H., Davidson, Susan, Anderson, Helen, Fletcher, Richard, Johnston, Patricia M., Rees, Malcolm(eds) Tertiary assessment & higher education studnet outcomes: policy, practice & research. Wellington : Ako Aotearoa pp91-96.

Campbell, A., Künnemeyer, R. and Prinsep, M. R. 2008. Staff perceptions of higher education science and engineering learning communities. Research in Science & Technological Education, Vol 26, No 3, pp279-294.

Campbell A. 2008. The creep of creationism – is it relevant to teaching earth sciences? Geological Society of New Zealand (Inc) 146, pp 23-26.

Campbell, A. 2007. Is intelligent design a scientific alternative to the theory of evolution? New Zealand Science Teacher 116 pp11-12.

Campbell, Alison. (2005). Intelligent Design? Radio New Zealand ‘Our Changing World’ interview 6th October.

Otrel-Cass, Kathrin, Earl, Kerry, Campbell, Alison, Cooke, Penelope. (2005). Evolution for Teaching Website evaluation report. NZ Science Teacher, Number 109, pp 27-29.

Buntting, Cathy, Coll, Richard Kevin and Campbell, Alison. 2005. Student views of concept mapping use in introductory tertiary biology classes. International Journal of Science and Mathematics Education. ISSN: 1573-1774 (Online).

Zepke Nick, Leach Linda, Prebble Tom, Campbell Alison, Coltman David, Dewart Bonnie, Gibson Maree, Henderson Judy, Leadbeater Jenny, Purnell Sue, Rowan Linda, Solomon Nika and Wilson Stewart. 2005. Improving tertiary student outcomes in the first year of study. Teaching & Learning Research Initiative.

Campbell, Alison. (2004). Book review: The flight of the huia. New Zealand Journal of Zoology, Vol.31, pp 379-380.

Campbell A, Cooke P, Earl K and Otrell-Cass K. (2004). A New Zealand “Evolution for Teaching” Online Resource. Teaching EARTH SCIENCES Vol 29, Number 3/4, pp 31-32.

Campbell, A.M., P. Cooke, K. Cass & K. Earl (2004) “Evolution for Teaching”.

I don’t see a single publication in experimental science in there. She doesn’t do research. She has no research publications. But if a genuine experimental biologist came into her classroom, that person would be marked down for disagreeing with her religion – the religion of materialism. The assumption of naturalism. Both of which are easily demonstrated as false simply by looking at the experimental evidence supporting the Big Bang theory, e.g. – redshift, cosmic microwave background radiation, light element abudnances, etc. But some people don’t let the science inform their worldview. They just write about teaching and then mark down actual experimental biologists who question their faith commitments to materialism and naturalism.

Here are some papers from Biologic Institute researchers:

D’Andrea-Winslow L, Novitski AK (2008) Active bleb formation is abated in Lytechinus variegatus red spherule coelomocytes after disruption of acto-myosin contractility. Integrative Zoology 3: 106-113. doi:10.1111/j.1749-4877.2008.00086.x

Axe DD, Dixon BW, Lu P (2008) Stylus: A system for evolutionary experimentation based on a protein/proteome model with non-arbitrary functional constraints. PLoS ONE 3: e2246. doi:10.1371/journal.pone.0002246

Sternberg RV (2008) DNA codes and information: Formal structures and relational causes. Acta Biotheoretica doi:10.1007/s10441-008-9049-6. PMID: 18465197

Gonzalez G (2008) Parent stars of extrasolar planets – IX. Lithium abundances. Monthly Notices of the Royal Astronomical Society, Online Early Articles doi:10.1111/j.1365-2966.2008.13067.x

Duren RW, Marks II RJ, Reynolds PD, Trumbo ML (2007) Real-time neural network inversion on the SRC-6e reconfigurable computer. IEEE Transactions on Neural Networks 18: 889-901. PMID: 17526353

Gonzalez G, Laws C (2007) Parent stars of extrasolar planets VIII. Chemical abundances for 18 elements in 31 stars. Monthly Notices of the Royal Astronomical Society 378: 1141-1152. doi:10.1111/j.1365-2966.2007.11867.x

Gravagne IA, Marks II RJ (2007) Emergent behaviors of protector, refugee and aggressor swarms. IEEE Transactions on Systems, Man and Cybernetics, Part B: Cybernetics 37: 471- 476. PMID: 17416173

Weinschenk JJ, Combs WE, Marks II RJ (2007) On the avoidance of rule explosion in fuzzy inference engines. International Journal of Information Technology and Intelligent Computing 1, #4.

Gonzalez G (2006) Condensation temperatures trends among stars with planets. Monthly Notices of the Royal Astronomical Society: Letters 367: L37-L41. doi:10.1111/j.1745-3933.2005.00136.x

Gonzalez G (2006) The sun’s interior metallicity constrained by neutrinos. Monthly Notices of the Royal Astronomical Society: Letters 370 : L90–L93.
doi:10.1111/j.1745-3933.2006.00197.x

Gonzalez G (2006) The chemical compositions of stars with planets: A review.
Publications of the Astronomical Society of the Pacific 118: 1494-1505 (invited review paper). doi:10.1086/509792

Gonzalez G (2005) Habitable zones in the universe. Origins of Life and Evolution of Biospheres 35: 555-606. doi:10.1007/s11084-005-5010-8

Keller D, Brozik JA (2005) Framework model for DNA polymerases. Biochemistry 44: 6877-6888. PMID: 15865433

Shapiro JA, von Sternberg R (2005) Why repetitive DNA is essential to genome function. Biological Reviews 80: 227-250. Review. PMID: 15921050

von Sternberg R, Shapiro JA (2005) How repeated retroelements format genome function. Cytogenetic and Genome Research 110: 108-116. PMID: 16093662

Axe DD (2004) Estimating the prevalence of protein sequences adopting functional enzyme folds. Journal of Molecular Biology 341: 1295-1315. PMID: 15321723

Lu H, Macosko J, Habel-Rodriguez D, Keller RW, Brozik JA, Keller D (2004) Closing of the fingers domain generates motor forces in the HIV reverse transcriptase. Journal of Biological Chemistry 279: 54529-54532. PMID: 15385563

Keller D, Swigon D, Bustamante C (2003) Relating single-molecule measurements to thermodynamics. Biophysical Journal 84: 733-738. PMID: 12547757

von Sternberg R, Cumberlidge N (2003) Autapomorphies of the endophragmal system in trichodactylid freshwater crabs (Crustacea: Decapoda: Eubrachyura). Journal of Morphology 256: 23-28. PMID: 12616572

Bustamante C, Keller D, Oster G (2001) The physics of molecular motors. Accounts of Chemical Research 34: 412-420. PMID: 11412078

D’Andrea-Winslow L, Strohmeier G, Rossi B, and Hofman P (2001) Identification of a Na/K/2Cl cotransporter (NKCC) in sea urchin coelomocytes: microfilament dependent surface expression mediated by hypotonic shock and cAMP. Journal of Experimental Biology 204: 147-156. PMID: 11104718

Gonzalez G, Brownlee D, Ward P (2001) The Galactic Habitable Zone: Galactic chemical evolution. Icarus 152: 185-200. doi:10.1006/icar.2001.6617

Axe DD (2000) Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors. Journal of Molecular Biology 301: 585-595. PMID: 10966772

von Sternberg R (2000) Genomes and form. The case for teleomorphic recursivity.
Annals of the New York Academy of Sciences 901: 224-236. PMID: 10818573

Wuite GJ, Smith SB, Young M, Keller D, Bustamante C (2000) Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404: 103-106. PMID: 10716452

Axe DD, Foster NW, Fersht AR (1998) A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease. Biochemistry 37: 7157-7166. PMID: 9585527

Axe DD, Foster NW, Fersht AR (1996) Active barnase variants with completely random hydrophobic cores. Proceedings of the National Academy of Sciences USA. 93: 5590-5594. PMID: 8643620

Gauger AK, Goldstein LS (1993) The Drosophila kinesin light chain. Primary structure and interaction with kinesin heavy chain. Journal of Biological Chemistry 268: 13657-13666. PMID: 8514798

Notice any differences between Alison’s papers and these papers? That’s right! These papers are science. Alison’s papers are not science. They are secular-left education policy. But all of these real scientists from Biologic would be “marked down” in her classroom – because philosophers and judges say that they must be marked down. Why assess the complicated science when you can just impose your religion by force on dissenters? It worked for the Catholic Church against Galileo. Maybe Alison doesn’t understand experimental science? Maybe ID papers are just too complicated for her to understand?

Since Alison mentions the bacterial flagellum by name, I thought that it might be useful for us to see a popular-level article on the bacterial flagellum written by an anonymous graduate student of biology. He has to be anonymous because of religious people like Alison who will mark him down for doing actual science that contradicts her faith. (I know who he is)

Excerpt:

As I mentioned in my previous essay, the synthesis of the bacterial flagellum is orchestrated by genes which are organised into a tightly ordered cascade in which expression of one gene at a given level requires the prior transcription of another gene at a higher level.

In Salmonella, the flagellar system has three classes of promoters — Class I, Class II, and Class III. This sequential transcription is coupled to the process of flagellar assembly. Class I contains only two genes in one operon, namely FlhD and FlhC. Class II consists of 35 genes across eight operons. These genes include those involved in the biosynthesis of the hook-basal-body and other components of the flagellum and export apparatus, as well as the regulatory genes FliA and FlgM. Those genes which are involved in the synthesis of the filament are controlled by virtue of the Class III promoters.

The Class I promoter is required to drive the expression of the enteric master regulator, FldH4C2. The Class II promoters are subsequently turned on by this master regulator in association with the sigma factor, σ70. The Class II promoters are responsible for the gene expression of the hook-basal-body subunits and its regulators, including σ28 (encoded by a gene called FliA) and its anti-sigma factor, FlgM. The sigma factor σ28 is, in turn, required in order to activate the class III promoters. Before the construction of the Hook-Basal-Body has been completed, one obviously does not want the flagellin monomers to be prematurely expressed. Thus, in order to inhibit the σ28, its anti-sigma factor FlgM keeps it away from the RNA polymerase holoenzyme complex. When, finally, the Hook Basal Body has been completed, the anti-sigma factor FlgM is secreted, remarkably, through the flagellar substructures which are produced by the expression of the Class II hook-basal-body genes. The Class III promoters are then finally turned on by the sigma factor σ28, and the flagellum is completed. These Class III promoters are responsible for the expression of flagellin monomers, the chemotaxis system and the motorforce generators. In all, more than 50 genes are necessary for flagellar self-assembly to take place.

The flagellar apparatus can basically be divided into two key components: the secretion system and the axial structure. As discussed in my previous piece, the key components of the axial structure are FlgG for the rod, FlgE for the hook, and FliC for the filament. Each of those has its own respective cap protein, by virtue of which it assembles. The cap protein for FlgG is FlgJ; for FlgE, it is FlgD; and for FliC, it is FliD.

The cap protein FliD remains at the tip of the filament in the finished product. Some other components of the axial structure — FlgB, FlgC and FlgF — connect the rod and MS ring complex. The hook and filament are connected by FlgK and FlgL.

The structural foundation of the flagellar apparatus is the MS ring complex. When the C ring and C rod attach to the cytoplasmic surface of the M ring, the complex begins to secrete flagellar proteins.

One particularly remarkable feature of the flagellar assembly is the construction of the rod structure (which is built through the peptidoglycan layer with the assistance of cap protein FlgJ). The outer membrane represents a road block such that it cannot continue to grow. Incredibly, the outer ring complex actually cuts a hole in the membrane to allow the hook to continue to grow beneath the FlgD scaffold until it reaches a specified critical length, upon which the substrates which are being secreted switch from the rod-hook mode to flagellin mode. FlgD is then replaced by hook associated proteins (or HAPs) and the filament continues to grow. This, of course, only works correctly in the presence of the cap protein FliD; otherwise the flagellin monomers are lost.

Alison thinks that that is creationism. Notice how often the Bible was cited? That’s right. It wasn’t. This guy is not even a young-earther, and he leans towards common descent, too. (UPDATE: He just post a pack of research against common descent last week and now he is leaning away from it)

Don’t read that Alison – it’s nasty science, and it would offend your beliefs! Just stick to writing the stuff you’re good at. And for Darwin’s sake, don’t try to debate the science with anyone who disagrees with you. Don’t read any books that disagree with you. And don’t read any research papers and cite them in your writings. Just mark the ID scientists down – that’s the safest way to silence them. Ram your religion down their throats. Who cares about evidence? Not you. Otherwise you would be reading theirs, and writing some of your own.

UPDATE: Lenny has a good post about biases at Come Reason.

News

NPR planned to hide $5 million donation from radical Muslim group from government

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(44 minutes)

Story from the left-wing Washington Post.

Excerpt:

An NPR fundraising executive said her organization would be willing to shield a would-be donor from a government audit by keeping the donor’s name anonymous, according to a series of surreptitiously recorded phone calls released on Thursday by a conservative activist.

Betsy Liley, NPR’s senior director of institutional giving, made the comments to a man posing as a trustee of a fictitious Muslim charity, which the man had said had connections to the Muslim Brotherhood, an Egypt-based group that has suspected ties to terrorists.

Liley’s conversations with the man were captured as part of a sting operation orchestrated by James O’Keefe, who has targeted the ACORN community group and Planned Parenthood with secret recordings.

O’Keefe secretly videotaped Liley’s boss, Ron Schiller, making demeaning comments about conservatives during a luncheon meeting set up to discuss what the NPR managers believed was a potential $5 million contribution. Liley was also at that meeting and briefly comments in the video.

Ron Schiller resigned from NPR on Tuesday for his role in the video scandal. The video’s release also led to the resignation on Wednesday of his boss, NPR chief executive Vivian Schiller.

In a lengthy follow-up phone call with Liley after the lunch, an O’Keefe associate posing as “Ibrahim Kasaam ” of the Muslim Education Action Center (a fictitious entity) expressed concerns that NPR, which receives government funding, would be subject to government audits or would have to disclose the source of its donations.

Liley responded, “If you were concerned about that, you might want to be an anonymous donor and we would certainly, if that was your interest, we would want to shield you from that.”

At another point, Kasaam asked Liley, “It sounded like you’re saying that NPR would be able to shield us from a government audit, is that correct?”

“I think that is the case, especially if you were anonymous, and I can inquire about that,” Liley said. She later informed Kasaam via e-mail that NPR’s management had cleared an anonymous donation from his group.

NPR had previously said, in the wake of the luncheon video, that it had “repeatedly refused” to accept donations from the organization.

NPR put Liley on administrative leave as a result of the video.

And they get millions of dollars of taxpayer money. It’s got to stop.